ArticleAnalytical chemistry2016
Optimized Fragmentation Regime for Diazirine Photo-Cross-Linked Peptides.
Article in Analytical chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 35 citations in OpenAlex.
- Towards a universal cross-linking mass spectrometry approach for protein structure analysis with homo-bi-functional photo-activatable cross-linkers.Communications biology · 2025Article
- Determining T-cell receptor binding orientation and Peptide-HLA interactions using cross-linking mass spectrometry.The Journal of biological chemistry · 2025Article
- Mass Spectrometric Identification of a Novel Factor XIIIa Cross-Linking Site in Fibrinogen.Proteomes · 2021Article
- A Diazirine-Modified Membrane Lipid to Study Peptide/Lipid Interactions - Chances and Challenges.Chemistry (Weinheim an der Bergstrasse, Germany) · 2021Article
- Reliable identification of protein-protein interactions by crosslinking mass spectrometry.Nature communications · 2021Article
- Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry.Nature communications · 2021Article
- Quantitative Photo-crosslinking Mass Spectrometry Revealing Protein Structure Response to Environmental Changes.Analytical chemistry · 2019Article
- Optimization Workflow for the Analysis of Cross-Linked Peptides Using a Quadrupole Time-of-Flight Mass Spectrometer.Analytical chemistry · 2019Article
- Cross-Linking/Mass Spectrometry Uncovers Details of Insulin-Like Growth Factor Interaction With Insect Insulin Binding Protein Imp-L2.Frontiers in endocrinology · 2019Article
- In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides.Journal of proteome research · 2018Article
- Chemical cross-linking in the structural analysis of protein assemblies.Methods (San Diego, Calif.) · 2018Review
- Protein Tertiary Structure by Crosslinking/Mass Spectrometry.Trends in biochemical sciences · 2018Review
- The Role of Electron Transfer Dissociation in Modern Proteomics.Analytical chemistry · 2018Review
- Article
- A Novel MS-Cleavable Azo Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS).Journal of the American Society for Mass Spectrometry · 2017Article
- Novel Concepts of MS-Cleavable Cross-linkers for Improved Peptide Structure Analysis.Journal of the American Society for Mass Spectrometry · 2017Article
- Optimizing the Parameters Governing the Fragmentation of Cross-Linked Peptides in a Tribrid Mass Spectrometer.Analytical chemistry · 2017Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Cross-linking/mass spectrometry has evolved into a robust technology that reveals structural insights into proteins and protein complexes. We leverage a new tribrid instrument with improved fragmentation capacities in a systematic comparison to identify which fragmentation method would be best for the identification of cross-linked peptides. Specifically, we explored three fragmentation methods and two combinations: collision-induced dissociation (CID), beam-type CID (HCD), electron-transfer dissociation (ETD), ETciD, and EThcD. Trypsin-digested, SDA-cross-linked human serum albumin (HSA) served as a test sample, yielding over all methods and in triplicate analysis in total 2602 matched PSMs and 1390 linked residue pairs at 5% false discovery rate, as confirmed by the crystal structure. HCD wins in number of matched peptide-spectrum-matches (958 PSMs) and identified links (446). CID is most complementary, increasing the number of identified links by 13% (58 links). HCD wins together with EThcD in cross-link site calling precision, with approximately 62% of sites having adjacent backbone cleavages that unambiguously locate the link in both peptides, without assuming any cross-linker preference for amino acids. Overall quality of spectra, as judged by sequence coverage of both peptides, is best for EThcD for the majority of peptides. Sequence coverage might be of particular importance for complex samples, for which we propose a data dependent decision tree, else HCD is the method of choice. The mass spectrometric raw data has been deposited in PRIDE (PXD003737).
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.